jvarkit

Biostar178713

split bed file into several bed files where each region is separated of any other by N bases

Usage

Usage: biostar178713 [options] Files
  Options:
    -d, --distance
      Distance between bed features.A distance specified as a positive 
      integer.Comma are removed. The following suffixes are interpreted : 
      b,bp,k,kb,m,mb 
      Default: 100
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
  * -o, --output
      Output file.zip .
    --version
      print version and exit

Keywords

• bed

See also in Biostars

• https://www.biostars.org/p/178713

Compilation

Requirements / Dependencies

• java compiler SDK 11. Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew biostar178713

The java jar file will be installed in the dist directory.

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/biostar/Biostar178713.java

Contribute

• Issue Tracker: http://github.com/lindenb/jvarkit/issues
• Source Code: http://github.com/lindenb/jvarkit

License

The project is licensed under the MIT license.

Citing

Should you cite biostar178713 ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030

Example

java -jar dist/biostar178713.jar -d 100000 -o out.zip in1.bed in2.bed 

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